# Script to compute final statistics

import sys

import os

# Loading .clstr file and building a dictionary from it:

def build_otus_dict1(filename) :

#handle = open("clusters.clstr", 'rU')

otus = dict()

handle = open(filename, 'rU')

i=0

for line in handle.readlines() :

if i > 2 :

splitted = line[:-1].split(' ')

val = splitted[0]

keys = splitted[1].split(',')

for k in keys :

otus[k] = val

i+=1

handle.close()

return otus

def build_otus_dict2(filename) :

# Loading .clstr file and building a dictionary from it:

#handle = open("clusters.clstr", 'rU')

handle = open(filename, 'rU')

otus = dict()

i=0

for line in handle.readlines() :

if i > 2 :

splitted = line[:-1].split(' ')

key = splitted[0]

values = splitted[1].split(',')

otus[key] = values

i+=1

handle.close()

return otus

def make_final_uctable(infilename, outfilename, num_markers) :

#outhandle = open("test.clstr",'w')

otus = build_otus_dict1(infilename)

outhandle = open(outfilename,'w')

for i in range(num_markers) :

handle = open(os.path.dirname(infilename)+"/map_"+str(i+1)+".uc",'rU')

for line in handle.readlines() :

splitted = line[:-1].split('\t')

otu = splitted[-1]

hit = splitted[0]

if hit != 'N' :

splitted[-1] = otus[otu]

string_to_write = '\t'.join(map(str,splitted))+'\n'

outhandle.write(string_to_write)

outhandle.close()

handle.close()

def make_final_otutable(infilename, otu_table_filename, num_markers) :

# Processing final OTU table

# Do read each file with otu table separately

otus = build_otus_dict2(infilename)

handle = open(os.path.dirname(infilename)+"/otu_table_1.txt",'rU')

barcodes = handle.readline()[:-1].split('\t')[1:]

#print barcodes

dictionaries = []

for i in range(1,num_markers+1) :

#print i

# Read otu table:

handle = open(os.path.dirname(infilename)+"/otu_table_"+str(i)+".txt",'rU')

d = dict()

j=0

for line in handle.readlines() :

if j > 0 : # Skip the First line

splitted = line[:-1].split('\t')

d[splitted[0]] = dict()

for l in range(1,len(splitted)) :

d[splitted[0]][barcodes[l-1]] = splitted[l]

j += 1

handle.close()

dictionaries.append(d)

summary = dict()

for k in otus.keys() :

summary[k] = dict()

for b in barcodes :

summary[k][b] = dict()

for i in range(1, len(dictionaries)+1) :

summary[k][b][i] = 0

for k in otus.keys() :

vals = otus[k]

for v in vals :

for i in range(1,len(dictionaries)+1) :

if v in dictionaries[i-1] :

for b in barcodes :

if b in dictionaries[i-1][v] :

summary[k][b][i] += int(dictionaries[i-1][v][b])

#print summary

outhandle = open(otu_table_filename, 'w')

string_to_write = "OTUId\t" + '\t'.join(map(str,barcodes))

print string_to_write

outhandle.write(string_to_write)

outhandle.write('\n')

# Now we write to output file:

for k in summary.keys() :

string_to_write = k

for b in summary[k].keys() :

maxnum = []

for v in summary[k][b].keys() :

maxnum.append(summary[k][b][v])

string_to_write += '\t' + str(max(maxnum))

print string_to_write

outhandle.write(string_to_write)

outhandle.write('\n')

outhandle.close()

def main():

argv = sys.argv

num_markers = int(argv[-1]) # Number of marker regions

otu_table_filename = argv[-2] # OTU table output filename

clstr_outfilename = argv[-3] # output file for final uc map table

clstr_infilename = argv[-4] # clustering table ("clusters.clstr")

make_final_uctable(clstr_infilename, clstr_outfilename, num_markers)

make_final_otutable(clstr_infilename, otu_table_filename, num_markers)

return 0

if __name__ == "__main__":

sys.exit(main())